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- EMDB-9975: Cryo-EM Structure of the Mammalian Tactile Channel Piezo2 -

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Basic information

Entry
Database: EMDB / ID: EMD-9975
TitleCryo-EM Structure of the Mammalian Tactile Channel Piezo2
Map data
Sample
  • Complex: homo-trimer of Piezo2
    • Protein or peptide: Piezo-type mechanosensitive ion channel component 2
  • Ligand: N-ACETYL-D-GLUCOSAMINE
Function / homology
Function and homology information


detection of mechanical stimulus involved in sensory perception / detection of mechanical stimulus / mechanosensitive monoatomic ion channel activity / monoatomic cation transport / monoatomic cation channel activity / response to mechanical stimulus / regulation of membrane potential / cellular response to mechanical stimulus / membrane => GO:0016020 / membrane / plasma membrane
Similarity search - Function
Piezo family / Piezo non-specific cation channel, R-Ras-binding domain / Piezo domain / Piezo non-specific cation channel, R-Ras-binding domain / Piezo
Similarity search - Domain/homology
Piezo-type mechanosensitive ion channel component 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsWang L / Zhou H / Zhang M / Liu W / Deng T / Zhao Q / Li Y / Lei J / Li X / Xiao B
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China31825014 China
National Natural Science Foundation of China31570730 China
CitationJournal: Nature / Year: 2019
Title: Structure and mechanogating of the mammalian tactile channel PIEZO2.
Authors: Li Wang / Heng Zhou / Mingmin Zhang / Wenhao Liu / Tuan Deng / Qiancheng Zhao / Yiran Li / Jianlin Lei / Xueming Li / Bailong Xiao /
Abstract: PIEZO2 is a mechanosensitive cation channel that has a key role in sensing touch, tactile pain, breathing and blood pressure. Here we describe the cryo-electron microscopy structure of mouse PIEZO2, ...PIEZO2 is a mechanosensitive cation channel that has a key role in sensing touch, tactile pain, breathing and blood pressure. Here we describe the cryo-electron microscopy structure of mouse PIEZO2, which is a three-bladed, propeller-like trimer that comprises 114 transmembrane helices (38 per protomer). Transmembrane helices 1-36 (TM1-36) are folded into nine tandem units of four transmembrane helices each to form the unusual non-planar blades. The three blades are collectively curved into a nano-dome of 28-nm diameter and 10-nm depth, with an extracellular cap-like structure embedded in the centre and a 9-nm-long intracellular beam connecting to the central pore. TM38 and the C-terminal domain are surrounded by the anchor domain and TM37, and enclose the central pore with both transmembrane and cytoplasmic constriction sites. Structural comparison between PIEZO2 and its homologue PIEZO1 reveals that the transmembrane constriction site might act as a transmembrane gate that is controlled by the cap domain. Together, our studies provide insights into the structure and mechanogating mechanism of Piezo channels.
History
DepositionJul 11, 2019-
Header (metadata) releaseSep 4, 2019-
Map releaseSep 4, 2019-
UpdateNov 6, 2019-
Current statusNov 6, 2019Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 10
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 10
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6kg7
  • Surface level: 10
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9975.png

Downloads & links

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Map

FileDownload / File: emd_9975.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.4 Å/pix.
x 320 pix.
= 448.32 Å		1.4 Å/pix.
x 320 pix.
= 448.32 Å		1.4 Å/pix.
x 320 pix.
= 448.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.401 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.69 / Movie #1: 10
Minimum - Maximum-19.493393000000001 - 49.744247000000001
Average (Standard dev.)0.077683754 (±1.3674089)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 448.32 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.4011.4011.401
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z448.320448.320448.320
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-19.49349.7440.078

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Supplemental data

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Sample components

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Entire : homo-trimer of Piezo2

EntireName: homo-trimer of Piezo2
Components
  • Complex: homo-trimer of Piezo2
    • Protein or peptide: Piezo-type mechanosensitive ion channel component 2
  • Ligand: N-ACETYL-D-GLUCOSAMINE

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Supramolecule #1: homo-trimer of Piezo2

SupramoleculeName: homo-trimer of Piezo2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human)
Molecular weightExperimental: 1 MDa

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Macromolecule #1: Piezo-type mechanosensitive ion channel component 2

MacromoleculeName: Piezo-type mechanosensitive ion channel component 2 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 325.984844 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASEVVCGLI FRLLLPICLA VACAFRYNGL SFVYLIYLLL IPLFSEPTKA TMQGHTGRLL QSLCITSLSF LLLHIIFHIT LASLEAQHR ITPAYNCSTW EKTFRQIGFE SLKGADAGNG IRVFVPDIGM FIASLTIWLV CRTIVKKPDT EEIAQLNSEC E NEELAGGE ...String:
MASEVVCGLI FRLLLPICLA VACAFRYNGL SFVYLIYLLL IPLFSEPTKA TMQGHTGRLL QSLCITSLSF LLLHIIFHIT LASLEAQHR ITPAYNCSTW EKTFRQIGFE SLKGADAGNG IRVFVPDIGM FIASLTIWLV CRTIVKKPDT EEIAQLNSEC E NEELAGGE KMDSEEALIY EEDLDGEEGM EGELEESTKL KILRRFASVA SKLKEFIGNM ITTAGKVVVT ILLGSSGMML PS LTSAVYF FVFLGLCTWW SWCRTFDPLL FGCLCVLLAI FTAGHLIGLY LYQFQFFQEA VPPNDYYARL FGIKSVIQTD CAS TWKIIV NPDLSWYHHA NPILLLVMYY TLATLIRIWL QEPLVQEEMA KEDEGALDCS SNQNTAERRR SLWYATQYPT DERK LLSMT QDDYKPSDGL LVTVNGNPVD YHTIHPSLPI ENGPAKTDLY TTPQYRWEPS EESSEKKEEE EDKREDSEGE GSQEE KRSV RMHAMVAVFQ FIMKQSYICA LIAMMAWSIT YHSWLTFVLL IWSCTLWMIR NRRKYAMISS PFMVVYANLL LVLQYI WSF ELPEIKKVPG FLEKKEPGEL ASKILFTITF WLLLRQHLTE QKALREKEAL LSEVKIGSQE LEEKEDEELQ DVQVEGE PT EKEEEEEEEI KEERHEVKKE EEEEVEEDDD QDIMKVLGNL VVALFIKYWI YVCGGMFFFV SFEGKIVMYK IIYMVLFL F CVALYQVHYE WWRKILKYFW MSVVIYTMLV LIFIYTYQFE NFPGLWQNMT GLKKEKLEDL GLKQFTVAEL FTRIFIPTS FLLVCILHLH YFHDRFLELT DLKSIPSKED NTIYSHAKVN GRVYLIINRL AHPEGSLPDL AIMNMTASLD KPEVQKLAES GEERPEECV KKTEKGEAGK DSDESEEEED EEEESEEEES SDLRNKWHLV IDRLTVLFLK FLEYFHKLQV FMWWILELHI I KIVSSYII WVTVKEVSLF NYVFLISWAF ALPYAKLRRA ASSVCTVWTC VIIVCKMLYQ LQTIKPENFS VNCSLPNENQ TN IPLHELN KSLLYSAPVD PTEWVGLRKS SPLLVYLRNN LLMLAILAFE VTVYRHQEYY RGRNNLTAPV SKTIFHDITR LHL DDGLIN CAKYFVNYFF YKFGLETCFL MSVNVIGQRM DFYAMIHACW LIGVLYRRRR KAIAEVWPKY CCFLACIITF QYFV CIGIP PAPCRDYPWR FKGAYFNDNI IKWLYFPDFI VRPNPVFLVY DFMLLLCASL QRQIFEDENK AAVRIMAGDN VEICM NLDA ASFSQHNPVP DFIHCRSYLD MSKVIIFSYL FWFVLTIIFI TGTTRISIFC MGYLVACFYF LLFGGDLLLK PIKSIL RYW DWLIAYNVFV ITMKNILSIG ACGYIGALVR NSCWLIQAFS LACTVKGYQM PEDDSRCKLP SGEAGIIWDS ICFAFLL LQ RRVFMSYYFL HVVADIKASQ ILASRGAELF QATIVKAVKA RIEEEKKSMD QLKRQMDRIK ARQQKYKKGK ERMLSLTQ E SGEGQDIQKV SEEDDEREAD KQKAKGKKKQ WWRPWVDHAS MVRSGDYYLF ETDSEEEEEE ELKKEDEEPP RKSAFQFVY QAWITDPKTA LRQRRKEKKK LAREEQKERR KGSGDGPVEW EDREDEPVKK KSDGPDNIIK RIFNILKFTW VLFLATVDSF TTWLNSISR EHIDISTVLR IERCMLTREI KKGNVPTRES IHMYYQNHIM NLSRESGLDT IDEHSGAGSR AQAAHRMDSL D SRDSISSC YTEATLLISR QSTLDDLDGQ DPVPKTSERA RPRLRKMFSL DMSSSSADSG SVASSEPTQC TMLYSRQGTT ET IEEVEAE AEEEVVEGLE PELHDAEEKE YAAEYEAGVE EISLTPDEEL PQFSTDDCEA PPSYSKAVSF EHLSFASQDD SGA KNHMVV SPDDSRTDKL ESSILPPLTH ELTASDLLMS KMFHDDELEE SEKFYVDQPR FLLLFYAMYN TLVARSEMVC YFVI ILNHM TSASIITLLL PILIFLWAML SVPRPSRRFW MMAIVYTEVA IVVKYFFQFG FFPWNKDLEI YKERPYFPPN IIGVE KKEG YVLYDLIQLL ALFFHRSILK CHGLWDEDDI VDSNTDKEGS DDELSLDQGR RGSSDSLKSI NLAASVESVH VTFPEQ PAA IRRKRSCSSS QISPRSSFSS NRSKRGSTST RNSSQKGSSV LSLKQKSKRE LYMEKLQEHL IKAKAFTIKK TLQIYVP IR QFFYDLIHPD YSAVTDVYVL MFLADTVDFI IIVFGFWAFG KHSAAADITS SLSEDQVPGP FLVMVLIQFG TMVVDRAL Y LRKTVLGKVI FQVILVFGIH FWMFFILPGV TERKFSQNLV AQLWYFVKCV YFGLSAYQIR CGYPTRVLGN FLTKSYNYV NLFLFQGFRL VPFLTELRAV MDWVWTDTTL SLSSWICVED IYAHIFILKC WRESEKRYPQ PRGQKKKKAV KYGMGGMIIV LLICIVWFP LLFMSLIKSV AGVINQPLDV SVTITLGGYQ PIFTMSAQQS QLKVMDNSKY NEFLKSFGPN SGAMQFLENY E REDVTVAE LEGNSNSLWT ISPPSKQKMI QELTDPNSCF SVVFSWSIQR NMTLGAKAEI ATDKLSFPLA VATRNSIAKM IA GNDTESS NTPVTIEKIY PYYVKAPSDS NSKPIKQLLS ENNFMNITII LFRDNVTKSN SEWWVLNLTG SRIFNQGSQA LEL VVFNDK VSPPSLGFLA GYGIMGLYAS VVLVIGKFVR EFFSGISHSI MFEELPNVDR ILKLCTDIFL VRETGELELE EDLY AKLIF LYRSPETMIK WTREKTN

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Macromolecule #2: N-ACETYL-D-GLUCOSAMINE

MacromoleculeName: N-ACETYL-D-GLUCOSAMINE / type: ligand / ID: 2 / Number of copies: 12 / Formula: NAG
Molecular weightTheoretical: 221.208 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.3
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

6865

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 2721959
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6kg7:
Cryo-EM Structure of the Mammalian Tactile Channel Piezo2

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